6ad5a3c086
removed color-space support
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which has been broken since 0.6.x
2013-02-12 10:21:17 -05:00
e5ab59db53
Multiple changes:
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1. Removed bwa.{h,c}. I am not going to finish them anyway.
2. Updated to the latest khash.h, which should be faster.
3. Define 64-bit vector and 128-bit integer/vector in utils.h.
2013-02-12 09:50:28 -05:00
13288e2dcd
code backup
2013-02-12 09:22:47 -05:00
dcb190069a
PE NOT working, yet
2013-02-11 16:10:14 -05:00
99907c98fb
separated and improved SAM printing code
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This is for the PE mode. The routines may also be useful for bwa-sw, but
probably I won't change the old code.
2013-02-11 15:29:03 -05:00
b6006cbe9d
skip orientations that are much smaller than best
2013-02-11 13:44:39 -05:00
4431e359e2
analyze isize distribution
2013-02-11 12:15:12 -05:00
987d4b4205
fixed a stupid bug in fastq reading
2013-02-11 11:27:35 -05:00
59eaf650ac
code backup
2013-02-11 10:59:38 -05:00
f4c0672800
move sort_and_dedup() to worker1()
2013-02-10 12:55:19 -05:00
c310fb7424
a little refactoring for PE support
2013-02-10 12:24:33 -05:00
cb55617f50
added a new line
2013-02-08 22:12:18 -05:00
95a79afe71
command-line prompt
2013-02-08 22:11:44 -05:00
829664d6b5
missing identical hits; improved sub_n
2013-02-08 17:55:35 -05:00
b2c7148dc9
consider the number of suboptimal hits
2013-02-08 17:20:44 -05:00
39607065e0
allow more seeds to be seen (thus slower..)
2013-02-08 16:56:28 -05:00
2848d3045a
more accurate chain weight
2013-02-08 15:34:25 -05:00
220fc39e9d
the previous change does not work... Fixed.
2013-02-08 14:51:24 -05:00
fdb0a7405f
better dealing with microrepeat
2013-02-08 14:46:57 -05:00
057b292dde
exclude identical hits
2013-02-08 14:18:39 -05:00
1bf1a674a8
minor improvement to mapQ
2013-02-08 13:43:15 -05:00
245505deed
minor improvement to mapQ approx.
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That is not good enough, but I am tired and need rest...
2013-02-07 22:09:58 -05:00
d8e4d57956
Don't use narrow band.
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I may retry this feature if the profilter indicates that this greatly helps.
2013-02-07 21:22:54 -05:00
d890c7997c
better treatment for micro-repeat
2013-02-07 21:20:36 -05:00
45b0d3423a
bugfix: when no seed hits found
2013-02-07 20:07:31 -05:00
cd6bd524d4
discard internal seeds shorter than half
2013-02-07 19:50:37 -05:00
83a49f3210
compute mapQ; extend from the longest seed
2013-02-07 17:15:45 -05:00
6ba11ab68c
no effective changes
2013-02-07 16:42:01 -05:00
ff3fea115c
write soft clip; added debugging code
2013-02-07 16:27:11 -05:00
27fdf6397d
single-end working! no mapQ, though
2013-02-07 15:52:36 -05:00
49f2bcc015
CIGAR is wrong, but the rest is okay
2013-02-07 14:57:22 -05:00
1fd51fc3f7
code backup
2013-02-07 14:36:18 -05:00
bfeb37c4de
code backup
2013-02-07 13:29:01 -05:00
5dc398cdef
start to write CLI
2013-02-07 13:13:43 -05:00
a09db69037
In bwtsw, replace the batch seq-reader with bseq
2013-02-06 17:12:27 -05:00
901d28d5f5
code backup
2013-02-06 15:03:09 -05:00
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
a9292d674d
a bit code cleanup
2013-02-06 13:59:32 -05:00
e65b2096f7
removed useless members
2013-02-06 12:25:49 -05:00
797a8c147e
sorting chains while filtering chains
2013-02-05 21:58:33 -05:00
a61288c768
separate CIGAR generation
2013-02-05 21:49:19 -05:00
14e6a7bdb9
fixed a silly bug in ksw_extend()
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Query return value is assigned to the target variable and vice versa...
2013-02-05 17:29:03 -05:00
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
2013-02-05 17:13:12 -05:00
86caae811e
added comments
2013-02-05 16:58:35 -05:00
1bc9712cd8
explicitly use bit to keep bt matrix
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This also simplifies backtracking.
2013-02-05 16:28:15 -05:00
7e1466c885
implemented NW backtrack
2013-02-05 16:05:53 -05:00
d91e320972
towards reimplementing banded NW alignment
2013-02-05 12:06:56 -05:00
7067af833d
fixed a silly bug on sorted merge
2013-02-05 00:41:07 -05:00
d6a73c9171
chain filtering apparently working
2013-02-05 00:17:20 -05:00
9d0cdb2d3c
unfinished chain filter
2013-02-04 17:23:06 -05:00
Heng Li